calculate_noise_threshold_method_statistics {noisyr} | R Documentation |
Function to tabulate statistics for different methods of calculating the noise threshold
Description
This function is used to tabulate and compare different combinations of similarity threshold and method to calculate the noise threshold for a given expression matrix.
Usage
calculate_noise_threshold_method_statistics(
expression,
similarity.threshold.sequence = 0.25,
method.chosen.sequence = noisyr::get_methods_calculate_noise_threshold(),
dump.stats = NULL,
...
)
Arguments
expression |
either an expression summary (as calculated by
|
similarity.threshold.sequence |
similarity (correlation or inverse distance) threshold(s) to be used to find corresponding noise threshold; can be a single value or a numeric vector; the default, 0.25 is usually suitable for the Pearson correlation (the default similarity measure) |
method.chosen.sequence |
methods to use to calculate the noise thresholds,
must be a subset of |
dump.stats |
name of csv to export different thresholds calculated (optional) |
... |
other arguments (for the boxplot methods) passed to |
Value
A tibble containing information on noise thresholds calculated using the input similarity thresholds and methods (optionally written in a csv file). The columns list the chosen method and similarity threshold, the minimum, mean, coefficient of variation, and maximum of the noise thresholds, and all the noise thresholds concatenated as a string.
See Also
Examples
expression.summary <- calculate_expression_similarity_counts(
expression.matrix = matrix(1:100, ncol=5),
method = "correlation_pearson",
n.elements.per.window = 3)
calculate_noise_threshold_method_statistics(expression.summary)